Yeah, it was the bug with only the flare-up effect appearing, and I fixed that up by altering the names of in the data\maps directory of FS2. (This bug fix was mentioned earlier on this thread).
This new bug (Primaries not usable on Herc Mark-2 and possibly other ships) is most definately caused by the ships.tbl, as when I remove only that file, I can use primaries again. Of course, I want the table there so that the effect is timed correctly. I just hope that I do not have to go alter it manualy, as I am NOT a modder by any means.
Did anyone else find this problem? Also, does anyone know if using the blue shockwaves would fix it? If not then I would just go ahead and install those, as I like the blue ones better anyway.
Oh, and I do not have any mods that could be causing this, so that's not an issue here.
Thanks for any help.